There has been a recent surge of interest in using mobility data from mobile phones to monitor social distancing and model the spread of SARS-COV-2, the virus that causes COVID-19. Despite several years of research in this area, standard frameworks for aggregating and making use of different data streams from mobile phones are lacking and difficult to generalize across data providers. Here, we provide a comprehensive set of guidelines for aggregation principles and procedures for different mobile phone data streams, and describe how aggregated data are used in research and policy. We argue that the principles of privacy and data protection are critical in assessing more technical aspects of aggregation, and should be an important central feature guiding partnerships with governments who make use of research products.